Small protein mediates inhibition of ammonium transport in Methanosarcina mazei – an ancient mechanism?

In the past decade, small open reading frames (sORFs) coding for proteins less than 70 amino acids (aa) in length have moved into the focus of Science. sORFs and corresponding small proteins have been recently identified in all three domains of life. However, the majority of small proteins remain functionally uncharacterized. While several bacterial small proteins have already been described, the number of identified and functionally characterized small proteins in archaea is still limited. In this study, we have discovered that the small protein 36 (sP36), which consists of only 61 aa, plays a critical role in regulating nitrogen metabolism in Methanosarcina mazei. The absence of sP36 significantly delays the growth of M. mazei when transitioning from nitrogen limitation to nitrogen sufficiency, as compared to the wild type. Through our in vivo experiments, we have observed that during nitrogen limitation, sP36 is dispersed throughout the cytoplasm; however, upon shifting the cells to nitrogen sufficiency, it relocates to the cytoplasmic membrane. Moreover, in vitro biochemical analysis clearly showed that sP36 interacts with high-affinity with the ammonium transporter AmtB 1 present in the cytoplasmic membrane during nitrogen limitation, as well as with the PII-like protein GlnK 1 . Based on our findings, we propose that in response to an ammonium up-shift, sP36 targets the ammonium transporter AmtB 1 and inhibits its activity by mediating the interaction with GlnK 1 . Importance Small proteins containing fewer than 70 aa, which were previously disregarded due to computational prediction and biochemical detection challenges, have gained increased attention in the scientific community in recent years. However, the number of functionally characterized small proteins, especially in archaea, is still limited. Here, by using biochemical and genetic approaches, we demonstrate a crucial role for the small protein sP36 in the nitrogen metabolism of M. mazei , regulating the ammonium transporter AmtB 1 according to nitrogen availability. This regulation might represent an ancient archaeal mechanism of AmtB 1 inhibition by GlnK, in contrast to the well-studied regulation in bacteria, which depends on covalent modification of GlnK.